I keep getting a loud clunk when swapping from front to rear brake. I use the front brake and then when the speed drops to 10mph or so I use the rear. When releasing the front and pressing the rear there is a loud clunk but not everytime. Is it because the brakes are linked? Or should I be doing some checks? The brakes work well but the noise makes me a little uneasy.

It depends on how confident you are with the spanners. From your description I would say it does need checking. I would put it on its main stand, then you can move the wheel, whilst looking to see if you can spot any thing that is making the noise, when you apply the rear brake. The rear caliper should have some movement, but should not have a loud clunking noise. If you cannot see anything then a visit to the workshop I think. It could also be the pads moving in the caliper thats causing the noise. Let us know what the outcome is.....

A click would be acceptable, as the pads are able to move within the caliper, but a clunk needs looking at. Before you ride it to a workshop though check the basics such as caliper, and rear arm security. take care!

Bike has covered just over 1000 miles as I have only had it a month. I have been riding in dynamic pro since the 600 mile service and only started to get the clunk then. maybe it is something to do with the ABS being turned right down or the linked system. It isn't the sound of the pads / floating disks moving. Will be weekend before I get chance to have a look at it as I'm on nights at the moment and trying to sleep in the daytime heat is about all I'm capable of at the moment. The clunk only happens after going from front brake lever to the rear brake. I can jump on the rear brake and it wont happen but gentle (normal) application does it almost every time. Is there some sort of change over valve in the ABS unit that allows the rear brake to work independently? The linked system is all new to me.

Is there some sort of change over valve in the ABS unit that allows the rear brake to work independently? The linked system is all new to me.

I'm not sure if BMW is any different than other manufacturers, but typically in a linked brake system there are an more than one pusher on each caliper. The system will apply lesser force to the brake not being activated by the rider.

So, for instance: If you squeeze the front brake lever, there will be two pistons closing the front brake, and only one piston closing the rear brake. If you apply the rear brake and no front brake, two pistons will clench the rear caliper and only one will close on the front caliper.

Difficult to explain. Easier to draw.

In my own experience, my Honda had three pistons in each caliper. The single rear piston that linked to the front would hesitate as I applied front brake and then suddenly clunk into place on the rear.